Chaste  Release::2018.1
T2SwapCellKiller.cpp
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34 */
35 
36 #include "T2SwapCellKiller.hpp"
37 
38 template<unsigned DIM>
40  : AbstractCellKiller<DIM>(pCellPopulation)
41 {
42  // Throw an exception if the population is not a VertexBasedCellPopulation
43  if (dynamic_cast<VertexBasedCellPopulation<DIM>*>(this->mpCellPopulation) == nullptr)
44  {
45  EXCEPTION("A T2SwapCellKiller should only be used together with a VertexBasedCellPopulation.");
46  }
47 }
48 
49 template<unsigned DIM>
51 {
52  /*
53  * This killer is different to other killers: it does not only check and label
54  * cells for apoptosis or death, it actually carries out vertex rearrangements
55  * and removes elements from the vertex mesh.
56  *
57  * We start with carrying out T2 swaps. Get the mesh and an element map.
58  * The static_cast will work since we already know it's a VertexBasedCellPopulation.
59  */
60  MutableVertexMesh<DIM,DIM>& mesh = static_cast<MutableVertexMesh<DIM,DIM>&>(this->mpCellPopulation->rGetMesh());
61  VertexBasedCellPopulation<DIM>* p_vertex_population = static_cast<VertexBasedCellPopulation<DIM>*>(this->mpCellPopulation);
62  VertexElementMap element_map(mesh.GetNumAllElements());
63 
64  bool recheck_mesh = true;
65  while (recheck_mesh == true)
66  {
67  // Note that whenever we call CheckForT2Swaps(), the element indices must run from zero up to mElements.size()-1
68  recheck_mesh = mesh.CheckForT2Swaps(element_map);
69  /*
70  * There might have maximally one T2 swap happened above, where a vertex element was removed from the
71  * mesh but the associated cell is still there. Here we check whether a new cell
72  * underwent a T2 swap and label it as dead as well as record its location and ID.
73  */
74  for (unsigned elem_index = 0; elem_index < element_map.Size(); elem_index++)
75  {
76  CellPtr p_cell = this->mpCellPopulation->GetCellUsingLocationIndex(elem_index);
77  if (element_map.IsDeleted(elem_index) && !(p_cell->IsDead()))
78  {
79  p_vertex_population->AddLocationOfT2Swap(mesh.GetLastT2SwapLocation());
80  p_vertex_population->AddCellIdOfT2Swap(p_cell->GetCellId());
81  p_cell->Kill();
82 
83  // There can't have been more than one new cell death, so leave the for loop here.
84  break;
85  }
86  }
87  }
88 
89 }
90 
91 template<unsigned DIM>
93 {
94  // No parameters to output, so just call method on direct parent class
96 }
97 
98 // Explicit instantiation
99 template class T2SwapCellKiller<1>;
100 template class T2SwapCellKiller<2>;
101 template class T2SwapCellKiller<3>;
102 
103 // Serialization for Boost >= 1.36
T2SwapCellKiller(AbstractCellPopulation< DIM > *pCellPopulation)
void OutputCellKillerParameters(out_stream &rParamsFile)
void CheckAndLabelCellsForApoptosisOrDeath()
bool CheckForT2Swaps(VertexElementMap &rElementMap)
unsigned GetNumAllElements() const
Definition: VertexMesh.cpp:616
#define EXCEPTION(message)
Definition: Exception.hpp:143
AbstractCellPopulation< SPACE_DIM > * mpCellPopulation
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
virtual void OutputCellKillerParameters(out_stream &rParamsFile)=0
c_vector< double, SPACE_DIM > GetLastT2SwapLocation()